RetrogeneDB ID: retro_mdom_1870

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:165086049..165086737(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000015979
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002508
• Aliases: None
• Description: None

Sequence

>retro_mdom_1870
ATGGCTGGGGATGCGGGAGGTCGTGGTTGCCCAGGCTCGGAGATGCTCCTGCACCCGGAGCTGCTCTCCCAGGACTTCCT
GCTGCTCACGCTGGAGCAGAAGAATATAGTTGTTGAAGAGGAAATAAAGATCAACAAAGATGACCTTACCGATTTCTGTG
TTCAACATGCCATACCATTGCCTCAAAGGGAATTACCAAAAAGTAGATGGGGGAAAATGATGGAAAAGAAAAGAGGGCAA
AATGAATTGAAAAATGAGCATAAAAGGGATATGAGTGTGGAAAGTTTACGGAAAAGACCCCTCGTTGTCTGATGGAAATT
CAACAAGTACAAGCATAAAAGTGAGAAAGACTGAAAATGGAACTAATGATCTTCTAAAACCTCCTCCATCAGTAGGCATT
ACTAACAATACCTTTAGGAAGTTACCACATTCAAACACTTCCTCCCTTATTCTGCCTTCTACCTTGCCTACAGACATTAA
AGTGGAAAGCAATAATGACACTAAACAGAACTATGTGTTAATGACTAGTAGGAGTACACTGGCCAATGTAAAATCACCAC
CATTATCTCCTGTTGGGGGAACTACTGTTGTGAAATTAAAGAGAACTGCTCCAAAAGAAGAAGCAGAATCAGTGAGTGAC
TTCAAGCCCACAGAAGCAAAAAGGAAGATCCAGCATGTTACATGGCCG

Alignment

ORF - retro_mdom_1870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGDAGGRGCPGSEMLLHPELLSQEFLLLTLEQKNIVVEEEIKINKDDLTDFYVQHAIPLPQRELPKSRW
          MAGDAGGRGCPGSEMLLHPELLSQ.FLLLTLEQKNIVVEEEIKINKDDLTDF.VQHAIPLPQRELPKSRW
Retrocopy MAGDAGGRGCPGSEMLLHPELLSQDFLLLTLEQKNIVVEEEIKINKDDLTDFCVQHAIPLPQRELPKSRW

Parental  GKMMEKKRGQNELKNEHKRNMSVESLR-KRPLIVFDGNSTSTSIKVRKTENGTNDRLKPPPSVGVTNNTF
          GKMMEKKRGQNELKNEHKR.MSVESLR.K.P....DGNSTSTSIKVRKTENGTND.LKPPPSVG.TNNTF
Retrocopy GKMMEKKRGQNELKNEHKRDMSVESLR>KDPSLS-DGNSTSTSIKVRKTENGTNDLLKPPPSVGITNNTF

Parental  RKLPHSNTSSLILPSTLPTDIKVESNNDTKQNHVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEA
          RKLPHSNTSSLILPSTLPTDIKVESNNDTKQN.VLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEA
Retrocopy RKLPHSNTSSLILPSTLPTDIKVESNNDTKQNYVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEA

Parental  ESVSDCKPTEAKRKIQHVTWP
          ESVSD.KPTEAKRKIQHVTWP
Retrocopy ESVSDFKPTEAKRKIQHVTWP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1870 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1870 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002508	3 retrocopies	retro_mdom_1092, retro_mdom_1870 , retro_mdom_41,